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- PDB-7cn3: 2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cn3 | ||||||
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Title | 2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid | ||||||
![]() | 2,5-dihydroxypyridine 5,6-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / oxidoreductase complex | ||||||
Function / homology | ![]() 2,5-dihydroxypyridine 5,6-dioxygenase / 2,5-dihydroxypyridine 5,6-dioxygenase activity / : / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, G.Q. / Tang, H.Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid Authors: Liu, G.Q. / Tang, H.Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 862.8 KB | Display | ![]() |
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PDB format | ![]() | 720 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cntC ![]() 7cupC ![]() 6koh S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 40589.938 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q88FY1, 2,5-dihydroxypyridine 5,6-dioxygenase |
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-Non-polymers , 6 types, 960 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/D6O.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/G6C.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/D6O.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/G6C.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-G6C / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density meas: 47.17 Mg/m3 / Density % sol: 47.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Succinic acid pH7.0 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 113279 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Num. unique obs: 5529 / CC1/2: 1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KOH ![]() 6koh Resolution: 2.2→27.59 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.69 Å2 / Biso mean: 35.8463 Å2 / Biso min: 14.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→27.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 30.4446 Å / Origin y: 33.405 Å / Origin z: 89.3904 Å
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Refinement TLS group |
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